Contacts of the helix formed by residues 46 - 65 (chain Q) in PDB entry 6FF7
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 46 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LYS* 5.8 9.9 - - + -
42Q LYS 5.3 1.6 - - - +
43Q VAL* 2.9 19.6 + - + +
45Q SER* 1.3 78.4 - - - +
47Q TRP* 1.3 62.3 + - - +
48Q PRO 3.6 0.7 - - - -
49Q ILE* 4.0 7.1 + - - +
50Q PHE* 3.9 15.4 + - - +
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Residues in contact with TRP 47 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43Q VAL 3.1 8.9 + - - +
44Q GLU* 4.0 17.0 - - + +
45Q SER 3.5 1.0 - - - -
46Q LEU* 1.3 76.9 - - - +
48Q PRO* 1.4 59.6 - - - +
50Q PHE* 3.2 8.5 + - - +
51Q ARG* 2.9 24.8 + - - +
136Q HIS 6.1 0.7 - - - -
137Q CYS 4.4 9.3 - - - +
138Q GLY* 4.3 23.3 - - - +
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Residues in contact with PRO 48 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32Q ALA* 4.4 19.4 - - + +
44Q GLU 4.7 3.8 - - - +
45Q SER 4.5 6.0 - - - +
46Q LEU 3.6 0.6 - - - -
47Q TRP* 1.4 78.4 - - - +
49Q ILE* 1.3 57.4 + - - +
51Q ARG* 3.6 10.3 - - + +
52Q ILE* 2.9 30.5 + - - +
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Residues in contact with ILE 49 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A PRO* 5.6 2.8 - - - +
64A GLU* 4.9 19.3 - - + +
65A HIS* 6.3 0.7 - - - -
68A LYS* 5.9 4.7 - - + -
29Q MET* 5.7 5.6 - - + +
32Q ALA* 4.7 17.1 + - + +
33Q GLU* 5.7 3.6 - - + +
45Q SER 5.1 2.7 + - - +
46Q LEU* 4.0 9.5 + - - +
47Q TRP 3.3 1.0 - - - -
48Q PRO* 1.3 74.2 - - - +
50Q PHE* 1.3 61.3 + - - +
52Q ILE* 4.3 3.4 - - - +
53Q HIS* 3.0 29.5 + - - +
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Residues in contact with PHE 50 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A PRO* 6.5 0.9 - - - -
46Q LEU 3.9 10.4 + - - +
47Q TRP* 3.2 9.8 + - - +
49Q ILE* 1.3 78.7 - - - +
51Q ARG* 1.3 56.7 + - - +
53Q HIS* 3.5 5.3 + - - +
54Q HIS* 2.9 29.3 + - - +
101Q CYS 4.9 2.3 - - - +
102Q CYS* 5.0 17.2 - - + +
136Q HIS 5.6 2.5 - - - +
137Q CYS* 4.4 15.9 - - - +
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Residues in contact with ARG 51 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196E TRP* 5.3 13.0 - - + -
47Q TRP 2.9 13.4 + - - +
48Q PRO* 3.6 13.2 - - + +
49Q ILE 3.3 0.2 - - - -
50Q PHE* 1.3 77.0 - - - +
52Q ILE* 1.3 56.9 + - - +
54Q HIS* 3.3 8.0 + - - +
55Q GLN* 2.9 27.5 + - - +
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Residues in contact with ILE 52 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25Q LEU* 5.4 5.3 - - + +
28Q LYS* 5.7 4.0 - - + +
29Q MET* 4.9 21.8 - - + +
32Q ALA* 5.7 2.2 - - + -
48Q PRO 2.9 18.2 + - - +
49Q ILE* 4.3 4.0 - - - +
51Q ARG* 1.3 73.3 - - - +
53Q HIS* 1.3 60.7 + - - +
55Q GLN* 3.8 5.4 - - - +
56Q LYS* 2.9 30.1 + - - +
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Residues in contact with HIS 53 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A PRO* 4.5 20.9 - - + -
49Q ILE 3.0 18.0 + - - +
50Q PHE* 3.9 5.4 - - - +
52Q ILE* 1.3 76.1 - - - +
54Q HIS* 1.3 57.4 + - - +
56Q LYS* 3.8 6.0 - - - +
57Q THR* 2.9 32.3 + - - -
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Residues in contact with HIS 54 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50Q PHE 2.9 17.5 + - - +
51Q ARG* 3.4 9.2 - - - +
52Q ILE 3.3 0.2 - - - -
53Q HIS* 1.3 77.2 - - - +
55Q GLN* 1.3 58.0 + - - +
57Q THR* 3.8 4.2 - - - -
58Q ARG* 2.9 30.2 + - - +
100Q LEU 5.4 2.7 - - - +
101Q CYS 3.9 20.4 - - - +
102Q CYS* 5.9 0.4 - - + -
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Residues in contact with GLN 55 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186E ALA* 3.3 23.2 - - + +
192E PHE* 5.0 13.2 - - + -
51Q ARG 2.9 16.2 + - - +
52Q ILE* 4.1 5.8 - - - +
53Q HIS 3.3 0.2 - - - -
54Q HIS* 1.3 76.2 - - - +
56Q LYS* 1.3 57.6 + - - +
58Q ARG* 4.2 5.6 - - - -
59Q TYR* 2.9 25.1 + - - +
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Residues in contact with LYS 56 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25Q LEU* 5.2 15.0 - - + -
52Q ILE 2.9 17.3 + - - +
53Q HIS* 3.8 7.2 - - - +
55Q GLN* 1.3 75.9 - - - +
57Q THR* 1.3 64.5 + - - +
59Q TYR* 3.2 7.1 + - - +
60Q ILE* 3.1 23.9 + - - +
83Q TYR 4.3 12.7 - - - +
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Residues in contact with THR 57 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53Q HIS 2.9 18.1 + - - -
54Q HIS* 4.0 5.2 - - - -
56Q LYS* 1.3 75.7 - - - +
58Q ARG* 1.3 57.1 + - - +
60Q ILE* 3.5 5.5 + - - +
61Q PHE* 2.8 29.2 + - - +
83Q TYR 4.5 6.8 + - - -
84Q ALA* 4.9 14.6 - - - +
85Q ASP* 5.0 9.0 - - - -
88Q LEU* 6.2 2.9 - - - -
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Residues in contact with ARG 58 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185E ASP 5.6 0.2 - - - +
186E ALA* 4.1 12.5 - - + +
54Q HIS 2.9 19.2 + - - +
55Q GLN* 3.8 6.1 - - - +
57Q THR* 1.3 75.3 - - - +
59Q TYR* 1.3 58.8 + - - +
61Q PHE* 3.4 8.1 - - - +
62Q ASP* 2.9 31.5 + - - +
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Residues in contact with TYR 59 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185E ASP 5.0 2.7 - - - +
186E ALA* 3.4 25.3 - - - +
187E SER* 5.6 0.2 - - - -
55Q GLN 2.9 19.3 + - - +
56Q LYS* 3.2 7.8 + - - +
58Q ARG* 1.3 77.4 - - - +
60Q ILE* 1.3 56.3 + - - +
62Q ASP* 3.8 1.0 - - - +
63Q LEU* 2.9 30.2 + - - +
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Residues in contact with ILE 60 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56Q LYS 3.1 15.1 + - - +
57Q THR 4.0 3.6 - - - +
59Q TYR* 1.3 75.5 - - - +
61Q PHE* 1.3 56.8 + - - +
63Q LEU* 3.2 7.1 + - - +
64Q PHE* 3.0 32.4 + - - +
78Q CYS* 5.6 7.6 - - + -
83Q TYR* 4.9 3.6 - - + +
84Q ALA* 4.5 20.0 - - + -
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Residues in contact with PHE 61 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57Q THR 2.8 19.9 + - - +
58Q ARG* 3.4 11.2 - - - +
60Q ILE* 1.3 76.5 - - - +
62Q ASP* 1.3 58.9 + - - +
64Q PHE* 5.5 0.4 - - - -
65Q TYR* 3.0 36.6 + - + +
89Q ILE* 6.2 3.8 - - + -
92Q TRP* 6.3 3.1 - - + -
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Residues in contact with ASP 62 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185E ASP 5.7 4.7 - - - +
58Q ARG 2.9 17.8 + - - +
59Q TYR* 3.8 1.6 - - - +
61Q PHE* 1.3 71.1 - - - +
63Q LEU* 1.3 59.3 + - - +
66Q LYS* 3.5 20.9 - - + +
67Q ARG* 3.1 26.2 + - - +
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Residues in contact with LEU 63 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59Q TYR 2.9 20.7 + - - +
60Q ILE* 3.2 10.1 + - - +
62Q ASP* 1.3 78.5 - - - +
64Q PHE* 1.3 60.5 + - + +
67Q ARG* 3.5 19.2 - - - +
68Q LYS 3.6 4.2 + - - -
69Q ALA* 3.7 9.4 + - - +
70Q ILE* 4.1 13.9 + - + -
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Residues in contact with PHE 64 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60Q ILE 3.0 14.8 + - - +
61Q PHE* 4.6 0.4 - - - +
63Q LEU* 1.3 78.6 - - + +
65Q TYR* 1.3 64.6 + - - +
66Q LYS 3.6 0.2 - - - -
68Q LYS* 3.3 21.0 + - - +
70Q ILE* 4.9 16.4 - - + +
71Q SER 5.4 0.4 - - - +
75Q TYR* 4.6 21.1 - - + -
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Residues in contact with TYR 65 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61Q PHE* 3.0 15.6 + - - +
64Q PHE* 1.3 80.0 - - - +
66Q LYS* 1.3 63.3 + - + +
68Q LYS* 4.4 4.7 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il